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Up in the skies above the Viridian Forest, Red watches the giant TR helicopter transform, and gasps that it has changed into a midair battle stadium. Just then, he feels an intense tightness gripping at his chest, and his hands begin to tremble.

Mewtwo wonders what is wrong, and Red explains that it is the same feeling he got when he stood face to face with Deoxys last time, the feeling of a vigorous thumping inside him which seems to make his all his blood backflow. Acknowledging this unique sensation he is experiencing again, Red is certain that Deoxys is waiting for them inside the TR helicopter.

As Charizard and Mewtwo edge closer to the midair battle stadium, the poles on the four corners of the arena suddenly send out beams of light to form a pyramidal shield and trap them in. Left with no choice but to descend, Red lands with Mewtwo onto a platform connected to the stadium through a flight of ascending stairs, and retreives Charizard into its Pokéball.

Almost immediately, the Pokéball shaped pattern in the center of the stadium opens up and Giovanni appears with Deoxys standing behind him. Red quickly gets into a combative stance, but the man calmly welcomes Red and Mewtwo, and wonders how Red feels to be towering over him at where he is standing. Red demands to know what he is talking about, and Giovanni grins that the platform Red has his feet on is meant for the champion.

Giovanni states that Red is the only person who has beaten him so far, and thus he feels such a set up will be most appropriate, with him being the challenger this time, and Red being the previous winner to be challenged again. The man then tosses off his jacket to reveal a white sleeveless pullover inside, claiming that he now fights not as the former Viridian Gymleader nor the leader of Team Rocket, but simply a trainer with no titles, against the Champion Red.

Red returns Giovanni's arrogant look with an angry glare of his, and pulls off his red jacket as well, revaling the black sleeveless pullover inside. He hops down from the platform to stand face to face with Giovanni, and Giovanni proposes their battle to be a simple one on one, with Mewtwo against Deoxys. Red accepts the challenge, and the two call forward their respective psychic mutants to the center of the stadium.

Speaking via telepathy, Mewtwo greets Deoxys and introduces itself, saying that while it has fought off the Deoxys-Divides at the Sevii Islands, it looks forward to experience the unknown space powers Deoxys claims to possess. Throughout the short conversation, Deoxys simply replies with some unfathomable sound, and begins curling up its tentacles into a combative stance while Mewtwo slowly forms his psychic spoon.

Then, without warning, Mewtwo swings its spoon against Deoxys, but the space Pokémon blocks it easily with its tentacles. Deoxys next thrusts its four tentacles forward, but Mewtwo swats them off with the spoon, and the two soon take the battle up into midair. Fending off yet another attack from Deoxys, Mewtwo tells Red that it will count on his directions in this battle, and hopes Red will give his best.

Mewtwo pulls its spoon back to prepare another strike, but Giovanni puts up his hand to signal to Deoxys, and the DNA Pokémon begins morphing rapidly between its four forms, from normal to speed, to defense, and finally to attack. Deoxys's sudden and quick appearance alteration stuns Mewtwo, and Deoxys, while in its attack form, delivers a powerful whip with its tentacles to send its foe crashing onto the ground.

Deoxys then returns to its normal form, and Mewtwo struggles to get up, wondering it it was what Red has told him. Giovanni confirms Mewtwo's suspicion, and says it is Deoxys's form change ability. Owing to the energy of the Ruby and Sapphire stone plates which have now extended from the Sevii Islands to reach Viridian, Deoxys is capable of freely morphing between its four forms at lightning speed, depending on the situation at hand.

Mewtwo wants to know what Red's battle strategy is, but to its shock, Red replies that he will not be using any. The boy states that Deoxys will easily counter whatever tactics they come up with by simply morphing into the appropriate form, and it will be pointless for strategies. Instead, he tells Mewtwo to charge up its strongest attack and count on brutal force alone. Mewtwo complies with what it is told, and sends out a powerful blast of energy towards where Red pinpoints, the crystalline organ on Deoxys's chest…